Mass Effect: Rediscovery
by ZarroKhaix
Summary: Hackett contacts Shepard about a very special mission that brings him back to Ilos. But this time he has to face an old ghost as well. With the Reapers hot on his tail, Shepard learns that some enemies are not so easy to fight. Especially when that enemy is his only hope. MShep/Liara. My first fanfic. R&R are welcome : .
1. Chapter 1

**Author's Notes**

Disclaimer - I do not own Mas Effect or any of its characters. All of it belongs to Bioware :(**  
**

**Chapter 1**

Shepard was bored. The captain's cabin was comfortable and everything but it was also lonely. The only companion he had was Larry, the space hamster, and Larry always hid in his little house whenever Shepard was around. Shepard really didn't understand why he did that. Despite being his owner, Liara seemed much closer to Larry than he was. Even Specialist Traynor was able to play with the rodent.

Shepard sighed and stretched his hands. It seemed so strange to have some peace and quiet when the rest of the galaxy was busy at war with the Reapers. In fact this few days of R&R had come only after Shepard had forged an alliance between the turians and krogans and also stopped an assassination attempt on the council by Cerberus.

Cerberus.

Even though the Reapers were the real enemy, Shepard couldn't help but feel that Cerberus was more of a danger to the Alliance's plan. Twice they had come close to destroying everything the Alliance had worked for.

Twice they had nearly defeated him.

But even Shepard couldn't fathom what the Illusive Man was planning. Once, he might have been able to guess his intention, but now the man was a former shadow of himself. He had been unable to distinguish the lines between his ambition for humanity and his concern for the species. In the end he was destroyed by it. Now all that was left was a monster that had taken the Illusive Man's place.

But the worst part of the entire coup attempt was that he had to come face to face with Kaidan.

Gun to gun.

It was close, too close. Thankfully, Kaidan believed him in the end and shot Udina, the real traitor. Shepard had never turned a gun on a fellow Alliance officer before, and certainly not on a friend. The question Kaidan asked him still haunted him;

_"Shepard, if I hadn't backed down there, would you have shot me?"_

Shepard had put on a fake smile and told Kaidan that he would never do that. But truthfully, he didn't know. He wasn't even sure what he would have done. And it haunted him. In the past he would have been able to distinguish right and wrong easily, but ever since the Reapers arrived everything had become so...grey.

Beep. Beep.

Shepard walked up to his intercom console and pressed the answer button. He hoped something interesting came up, not another fight with the Reapers or Cerberus, so he could get his mind off thing for a few hours.

"Hello" Shepard answered lazily.

"Commander, I have an incoming call from Admiral Hackett" replied EDI, the smooth-talking AI of the Normandy "I've patched him to the comm room"

Shepard sighed inwardly. There went his relaxing day. Admiral Hackett only contacted him if he had a mission.

"Thanks EDI" Shepard answered her "I'm on my way"

He shut off the intercom and went to change into his standard Alliance uniform. It wasn't appropriate to talk to the Admiral in a hoodie, even if it had the N7 insignia on it.

_Well at least I won't be bored anymore _he thought to himself as he headed for the elevator.

"Commander" Hackett said by way of greeting as he appeared as a blue hologram.

Shepard saluted him "Sir"

Hackett returned the salute and after moment both relaxed.

"What can I do for you, sir?" Shepard was curious as to why Hackett had contacted him. Perhaps the asari were in need of assistance. Or they had finally heard word of the quarians.

"Shepard, one of our survey stations in the Attican Traverse went silent a couple of days ago" Hackett began "They were scanning teams, alert for any presence of Reapers in the system"

"What system were they in?" Shepard asked.

"The Pangaea Expanse" Hackett let the information sink in.

"Ilos" Shepard whispered, before looking at Hackett "why have a survey system in the Pangaea Expanse? We have no colonies there"

"After the first Normandy managed to make it to Ilos, the Council decided to try and reclaim the system" Hackett explained "A group of highly paid explorers managed to imitate the feat and the Council decided to give the system to the Alliance as a gift for saving their asses three years ago"

"We had several researchers there trying to explore the ruins to give us more clues to the prothean's history and find proof of your claims about the Reapers" Hackett continued "but now they and the survey team have dropped out of contact"

"The Reapers?" asked Shepard, though he knew the answer to the question.

"Yes, we believe so, Commander" Hackett paused for a moment before continuing "Our lead researcher there, Doctor Salyam, said they had made an interesting discovery on the planet"

"What was it?" asked Shepard, curious.

"The details are vague but he mentioned something about a Reaper not being a Reaper and changing the war" Hackett answered "I know Salyam, Commander, he isn't the type to boast or exaggerate"

"You want me to rescue him?"

"And find out what he discovered" Hackett added "Shepard if this can help the Crucible, help the war, we have to find out"

"I'll get it done, sir" Shepard assured him

"One more thing, Commander" Hackett sighed before looking back at him "The researchers managed to uncover something else"

"What is it, Admiral?"

"A ship, Alliance, and one we believed was missing for nearly thirty years" Hackett replied "During the First Contact War, we sent out a dozen ships to do space reconnaissance in unknown systems. Many of these ships never made it back. The SSV Ergo, the ship on Ilos, was one of them"

"I see, sir"

"No you don't, Shepard" Hackett looked at Shepard directly in the eye "The SSV Ergo, it's captain...was your father"

_And just when I thought I had seen it all._


	2. Chapter 2

**Authors Notes**

I forgot to mention my Shepard's specifications last time, so here it is:

Background: Spacer, War Hero

Alignment: Paragon

Love Interest : Liara

History : Saved Kaidan, Saved Council, Destroyed Collector Base

And that's about it. Enjoy :)

Disclaimer -

Admiral Hackett : Commander.

Shepard : Sir?

Admiral Hackett : I just wanted you to know that Mass Effect and all of it's characters are owned by Bioware. Remember that.

Shepard : Yes, Sir!

**Chapter 2**

"We should be nearing the Mu Relay soon, commander" Joker said to Shepard, who was pacing behind him restlessly.

Shepard merely nodded and continued to pace. Hackett's revelation had not only rattled Shepard but left him confused. As far as Shepard knew, his father had been dead for nearly thirty years...at least that was what his mother told him.

Father.

Shepard had been very young when his father died. He barely had any memories of the man. No, scratch that, he didn't have any memories of the man. All he knew about Captain Marcus Shepard was the things he had learned from others. Marcus Shepard had been part of the Alliance Navy, married to Hannah Shepard for four years, and went missing in action, presumed killed in action, during the First Contact War. Shepard's mother rarely talked about the man, and whenever Shepard tried to ask about him, she would quickly switch to a different topic.

"Never thought I'd be going to Ilos again" Joker's voice broke through Shepard's thoughts.

"Same here" Shepard replied

"After the Battle of the Citadel, the Council sent out part of its fleet to secure the region from the Terminus Systems" EDI informed them as she continued scanning for enemy presence "However, after the Reapers attacked, whatever forces that were protecting the Mu Relay was recalled for defense on more urgent sectors"

"So basically, we're all alone right now" Joker said and then muttered under his breath "yep, definitely like last time"

"Shepard, it would be wise to search the survey station before landing on Ilos" EDI advised "The research team would have moved constantly, but the survey station should have a register on their last known location"

"Understood" Shepard replied "Joker?"

"Everybody, hold on!"

The Normandy lurched to the side as Joker swerved the ship towards the Mu Relay. In a few seconds the ship was enveloped in a blinding blue light. Shepard felt as if his whole body was being pulled forward. Then, as fast as it happened, it was over.

"Welcome back" Joker muttered sarcastically.

"Scanning" EDI paused for a moment "No Reaper forces detected in the immediate area"

"Good" Shepard looked out the viewport. Everything looked so peaceful out there.

"Joker, get us to the survey stations" He continued then hit the intercom button "Cortez, prep the shuttle"

"Aye, sir" Steve Cortez's voice answered back at him.

"James, Liara, Kaidan" Shepard hit the intercom once again "Suit up, we're going in"

"On my way, Shepard" Liara answered.

"Yes, Commander" that was Kaidan.

"Roger, loco" James replied.

"Shepard, my scanning systems cannot detect the inside of that station with the lockdown in place" EDI warned him "there may be Reaper forces inside"

"Acknowledged" Shepard answered her as he left the bridge.

_Now, let's go get some answers._

"So what are we looking for down here, loco?" asked James as he took a seat in the shuttle. Kaidan stood next to him while Liara leaned against the doorway.

"The research team on Ilos were on the move constantly" Shepard replied as he checked his weapon once again "the best way we can find their location is by searching through the records on the survey station. Other than that, this station has also gone dark, we're here to investigate"

"It doesn't make sense for a station wide lockdown if the Reapers attack" Kaidan replied, obviously uneasy "They would just destroy the station not scan room to room for people"

"Or, they may have been searching for something" Liara answered him "I'm more interested in the Alliance ship that crashed on Ilos, what do we know about it?"

"Nothing much other than its mission and it's captain" Shepard looked at her and noted concern in her eyes. She was worried about him. "But the ship is a secondary objective, for now let's focus on finding out what happened to this station and finding Doctor Salyam"

"Aye, aye" Kaidan replied.

"We're getting close, get ready" Cortez cut their conversation short "there's a small docking port near the lower hangar, I'll drop you there"

"Understood"

James got out of the shuttle first followed closely by Shepard and Kaidan and finally Liara. The docking port was deserted. However, there wasn't any sign of battle. It was as if everyone had just got up and left.

Which gave Shepard a very bad feeling.

"James, take point" He motioned the Lieutenant to move up front.

James nodded and began scouting the area. They slowly made their way out of the docking port and into the station itself.

"It's too quiet in here" Kaidan whispered through the comm channel.

"Reminds me of how the collectors used to abduct those colonists" Shepard replied as he followed James up the stairs and into the next room "No battle, just pickup"

"Yeah, I remember"

"Hold on" Liara called out and they stopped.

"You found something?" Shepard asked her.

"No, but I'm detecting high-levels of nano-toxic gases in the next room" Liara answered as she scanned with her omni-tool.

"Nano-toxic gases?"

"Used as a way to deliver small antibiotics and such into the body" Liara replied "In small amounts they are very useful but in large amounts they are lethal, especially if they are released into oxygen-infused air"

"So that's what caused the lockdown?" Kaidan asked her.

"Most probably, they could have also killed the staff on this station"

"They did" James motioned for them to look through the door window.

"What did you find?" Shepard asked him as he looked through the window. He almost puked when he saw it. A body, probably a female, was lying in the room. Her face looked like it had been eaten out.

"Yes, that's the effect of nano-toxic gases" Liara grimaced as she saw the body.

"Is there a way to get past it, or deactivate it?" Shepard looked away, he couldn't bear it anymore.

"No, we'll have to go around and find another way into the engineering department" Liara answered him "We should be able to clear the ventilation from there"

"Understood" Shepard opened a channel to the Normandy "EDI can you give me the location of the engineering department?"

"Yes, Shepard" she replied and a moment later Shepard's hud indicated a new marker.

"Let's go"

"So how does this station have nano-toxic gases?" Shepard asked as they neared the engineering room "It's just a survey station after all"

"Nano-toxic gases are present in the smallest medical devices, even medi-gel" Liara replied "If this station had a storage of medi-gel, than whoever killed these people had probably gotten their supply from there"

"Oh"

"Shepard, you really should read up on these things"

Shepard gave her a small smile "Why would I do that when I have you?"

She huffed, but smiled back at him "You can be so stubborn"

James cleared his throat and the two of them looked at him.

"Not to interrupt" He said "but we're here"

He pointed to the door just to their left. Above it read;

ENGINEERING DEPARTMENT

HEAD OF ENGINEERING DEPARTMENT : MALCOLM CONNELY

"Good" Liara said and moved up "give me a moment and I should be able to clear the air"

She entered the room slowly with Shepard and James flanking her.

"Get to work, Liara, we'll cover you"

Shepard scanned the area. He had a feeling they were being watched. They waited a few minutes until Liara turned away from the console.

"Done, we should be in the clear now" Liara walked back towards them.

"Good"

"Shepard" it was Kaidan, he was guarding the outside "I'm detecting movement here, I think I'm gonna check it-ARGH!"

"Kaidan!" Shepard dashed out of the room, to see Kaidan on the floor and man standing above him.

The moment the man saw Shepard, he ran the opposite way. Shepard ran towards Kaidan.

"How bad?" Shepard asked him.

"I'll be fine, he's getting away!' Kaidan groaned as he sat up.

"Liara, help Kaidan" Shepard said as he got up "James, with me!"

The assailant had a good head start, but James and Shepard were much faster runners than him. They nearly had him until he entered a door that locked itself behind him.

"Damnit" Shepard cursed as he came to halt just before he could crash into the door.

"Over here, Loco!" James entered a different room before crossing into the one the assailant went. Shepard followed him. They eventually cornered the man into a small storage room with no exit other than the one they came through.

Shepard and James raised their guns towards the assailant.

"You've got nowhere to go, pal" Shepard said as he moved closer "Give it up"

The man turned towards him and Shepard noted that his eyes were unfocused, like those of a madman. The man pulled out a gun and Shepard raised his higher.

"Drop it" Shepard warned him.

"YOU CANNOT STOP ME!" The man roared at him...in a voice akin to the Reapers. Shepard and James looked at each other confused. "I WILL BE FREE!"

"W-What?" Shepard asked but, too late, the man raised the pistol to his head "Wait!"

The shot rang across the room, and the man dropped like a puppet whose strings had been cut.

"Damn" James muttered as he lowered his gun "What was that all about?"

Shepard walked to inspect the body. The man had a name tag on him.

"Any idea who he is?" James asked he walked towards Shepard.

"Yeah" Shepard answered slowly "Jhong-Ryu, the overseer of this station"

_What the hell is going on in this place?_


End file.
